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Sample GSM205435 Query DataSets for GSM205435
Status Public on Jun 27, 2007
Title Col_ leaf_ wildtype_rep02
Sample type genomic
Source name leaf tissue (approx. 12th true leaf)
Organism Arabidopsis thaliana
Characteristics Columbia
Biomaterial provider Jerzy Paszkowski
Treatment protocol NA
Growth protocol Plants were grown in soil under short-day conditions (8 h light/16 h dark) at 22°C.
Extracted molecule genomic DNA
Extraction protocol Per entry, two biological replicates of leaf tissue (approx. 12th true leaf) from 9-12 plants were frozen in liquid nitrogen. DNA was CTAB extracted and isopropanol precipitated, RNase A and Proteinase K treated, re-extracted and ethanol precipitated.
Label Two replicates per entry with 7.5 µg DNA were fragmented; end labeled, and hybridized on Affymetrix ATH1 arrays as recommended (Affymetrix).
Label protocol Affymetrix Double standed DNA Labelling reaction.
Manufacturer's protocol, see manufacturer's web site
Hybridization protocol Manufacturer's protocol, see manufacturer's web site
Scan protocol Manufacturer's protocol, see manufacturer's web site
Description Two replicate 3 µg genomic DNA samples of 2nd generation met1-3, 4th generation met1-3 and Col-0 were sheared by sonication and methylated DNA was immunoprecipitated, as previously described (Weber et al., 2005), and amplified following the chromatin immunoprecipitation assay protocol (Affymetrix).
Data processing The .CHP files were generated with the Affymetrix GCOS software for preliminary analysis of the methylation values. The raw .CEL files were directly used for the methylation analysis. Using the gcRMA method, background adjustments were made and background-adjusted values from the six ATH1 datasets were quantile normalized using the Bioconductor package of R. Average signal intensities were determined in log2 scale per probe set. Contrast coefficient ratios for all pair-wise comparisons were calculated as follows: met1-3 2nd/Col-0, met1-3 4th/Col-0, and met1-3 4th/met1-3 2nd. Corrections for multiple comparisons at the 5% false discovery rate (FDR) were performed and significant differences were detected using Fisher’s test. For each probe set, three outcomes (significantly hypermethylated, no difference, and significantly hypomethylated) were possible per comparison, creating 27 possible methylation profiles analyzed at the 5% FDR level.
Submission date Jun 25, 2007
Last update date Aug 28, 2018
Contact name Jon Reinders
Phone +41 22 379 3029
Fax +41 22 379 3107
Organization name Universite de Geneve
Department Department of Plant Biology
Lab Laboratory of Plant Genetics
Street address 30 quai Ernest-Ansermet
City Genève
State/province Genève
ZIP/Postal code CH-1211
Country Switzerland
Platform ID GPL198
Series (1)
GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
Reanalyzed by GSE119083

Data table header descriptions
VALUE GCOS-processed signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 45.6808 A 0.783556
AFFX-BioB-M_at 7.48609 A 0.83416
AFFX-BioB-3_at 4.53445 A 0.979995
AFFX-BioC-5_at 30.7376 A 0.83416
AFFX-BioC-3_at 10.0036 A 0.876469
AFFX-BioDn-5_at 5.62952 A 0.97611
AFFX-BioDn-3_at 42.0369 A 0.834181
AFFX-CreX-5_at 25.5782 A 0.814932
AFFX-CreX-3_at 81.9131 A 0.588688
AFFX-DapX-5_at 153.25 P 0.0151826
AFFX-DapX-M_at 2.47728 A 0.999497
AFFX-DapX-3_at 5.01636 A 0.99315
AFFX-LysX-5_at 55.73 A 0.673019
AFFX-LysX-M_at 27.8809 A 0.724889
AFFX-LysX-3_at 40.16 A 0.804734
AFFX-PheX-5_at 27.8381 A 0.860601
AFFX-PheX-M_at 6.69892 A 0.995986
AFFX-PheX-3_at 3.57639 A 0.993832
AFFX-ThrX-5_at 30.954 A 0.686337
AFFX-ThrX-M_at 9.81974 A 0.794329

Total number of rows: 22810

Table truncated, full table size 684 Kbytes.

Supplementary file Size Download File type/resource
GSM205435.CEL.gz 1.4 Mb (ftp)(http) CEL
GSM205435.CHP.gz 122.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file
Processed data provided as supplementary file

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